[Debian-med-packaging] Psortb has errors in Perl testsuite

[Andreas Tille]

Hi,

I'd like to package psortb[1] which contains some Perl modules.
Unfortunately the Build-Time test fails.  My poor Perl knowledge tells
me that this might be a path issue but my be I'm asking here for a hint
how to solve this:

...
Result: PASS
make[2]: Leaving directory '/build/psortb-3.0.4+dfsg/algorithm-hmm'
make[2]: Entering directory '/build/psortb-3.0.4+dfsg/bio-tools-psort-svmloc'
Manifying 1 pod document
make[2]: Leaving directory '/build/psortb-3.0.4+dfsg/bio-tools-psort-modhmm'
PERL_DL_NONLAZY=1 PERL_USE_UNSAFE_INC=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t
PERL_DL_NONLAZY=1 PERL_USE_UNSAFE_INC=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, '../blib/lib', '../blib/arch')" t/*.t

#   Failed test 'use Bio::Tools::PSort::SVMLoc;'
#   at t/svmloc.t line 11.
#     Tried to use 'Bio::Tools::PSort::SVMLoc'.
#     Error:  Can't load '/build/psortb-3.0.4+dfsg/bio-tools-psort-svmloc/../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so' for module Bio::Tools::PSort::SVMLoc: /build/psortb-3.0.4+dfsg/bio-tools-psort-svmloc/../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so: undefined symbol: _ZN7DataSet12getAttributeEi at /usr/lib/x86_64-linux-gnu/perl/5.24/DynaLoader.pm line 187.
#  at t/svmloc.t line 11.
# Compilation failed in require at t/svmloc.t line 11.
# BEGIN failed--compilation aborted at t/svmloc.t line 11.

#   Failed test 'use Bio::Tools::PSort::SVMLoc::DataSet;'
#   at t/svmloc.t line 12.
#     Tried to use 'Bio::Tools::PSort::SVMLoc::DataSet'.
#     Error:  Attempt to reload Bio/Tools/PSort/SVMLoc.pm aborted.
# Compilation failed in require at /build/psortb-3.0.4+dfsg/bio-tools-psort-svmloc/../blib/lib/Bio/Tools/PSort/SVMLoc/DataSet.pm line 7.
# BEGIN failed--compilation aborted at /build/psortb-3.0.4+dfsg/bio-tools-psort-svmloc/../blib/lib/Bio/Tools/PSort/SVMLoc/DataSet.pm line 7.
# Compilation failed in require at t/svmloc.t line 12.
# BEGIN failed--compilation aborted at t/svmloc.t line 12.
& not defined at t/svmloc.t line 22.
        (in cleanup) & not defined at /build/psortb-3.0.4+dfsg/bio-tools-psort-svmloc/../blib/lib/Bio/Tools/PSort/SVMLoc.pm line 46.
        Bio::Tools::PSort::SVMLoc::AUTOLOAD("DESTROY", Bio::Tools::PSort::SVMLoc=HASH(0x55d74896cc70)) called at /build/psortb-3.0.4+dfsg/bio-tools-psort-svmloc/../blib/lib/Bio/Tools/PSort/SVMLoc.pm line 47
        Bio::Tools::PSort::SVMLoc::AUTOLOAD(Bio::Tools::PSort::SVMLoc=HASH(0x55d74896cc70)) called at /usr/share/perl/5.24/Carp.pm line 167
        eval {...} called at /usr/share/perl/5.24/Carp.pm line 167
        Bio::Tools::PSort::SVMLoc::new("Bio::Tools::PSort::SVMLoc", "Model", "sample.model", "FreqPatt", "fre_patterns.txt") called at t/svmloc.t line 22
# Looks like you planned 15 tests but ran 3.
# Looks like you failed 2 tests of 3 run.
# Looks like your test exited with 255 just after 3.
t/svmloc.t .. 
1..15
not ok 1 - use Bio::Tools::PSort::SVMLoc;
not ok 2 - use Bio::Tools::PSort::SVMLoc::DataSet;
ok 3 - Loaded SVMLoc
Creating new Bio::Tools::PSort::SVMLoc
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 14/15 subtests 
...


Line 11 of bio-tools-psort-svmloc/t/svmloc.t is

   BEGIN { use_ok('Bio::Tools::PSort::SVMLoc'); }


and the dynamic library that can not be loaded exists:

# ls -l /build/psortb-3.0.4+dfsg/bio-tools-psort-svmloc/../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so
-rwxr-xr-x 1 pbuilder pbuilder 170824 Apr 19 08:48 /build/psortb-3.0.4+dfsg/bio-tools-psort-svmloc/../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so


Any idea how to get this test working properly?

Kind regards

       Andreas.

PS: To build psortb you need to enable experimental in
    sources.list to get libsquid-dev (>= 1.9g+cvs20050121-9~)
    and libhmmer2-dev (>= 2.3.2+dfsg-2~) [the latter was just
    uploaded - may be there is some delay]


[1] https://anonscm.debian.org/git/debian-med/psortb.git

-- 
http://fam-tille.de